IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Mol. Cell. Biol. (0270-7306) 2004 imex curation McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org 29-OCT-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom ms participant Identification by mass spectrometry ms participant McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org Accepted 2007-JUN-22 by DAVET. Mol. Cell. Biol. (0270-7306) 2004 Only protein-protein interactions imex curation Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Mol. Cell. Biol. (0270-7306) 2004 imex curation McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org 29-OCT-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot McConnell AD., Gelbart ME., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complex purified by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column. ttsukiya@fhcrc.org Accepted 2007-JUN-22 by DAVET. 29-OCT-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2004 Only protein-protein interactions imex curation isw2_yeast ISWI chromatin-remodeling complex ATPase ISW2 ISW2 Imitation switch protein 2 YOR304W protein protein yeast Saccharomyces cerevisiae Baker's yeast MTTQQEEQRSDTKNSKSESPSEVLVDTLDSKSNGSSDDDNIGQSEELSDKEIYTVEDRPPEYWAQRKKKFVLDVDPKYAKQKDKSDTYKRFKYLLGVTDLFRHFIGIKAKHDKNIQKLLKQLDSDANKLSKSHSTVSSSSRHHRKTEKEEDAELMADEEEEIVDTYQEDIFVSESPSFVKSGKLRDYQVQGLNWLISLHENKLSGILADEMGLGKTLQTISFLGYLRYVKQIEGPFLIIVPKSTLDNWRREFLKWTPNVNVLVLHGDKDTRADIVRNIILEARFDVLITSYEMVIREKNALKRLAWQYIVIDEAHRIKNEQSALSQIIRLFYSKNRLLITGTPLQNNLHELWALLNFLLPDIFGDSELFDEWFEQNNSEQDQEIVIQQLHSVLNPFLLRRVKADVEKSLLPKIETNVYVGMTDMQIQWYKSLLEKDIDAVNGAVGKREGKTRLLNIVMQLRKCCNHPYLFEGAEPGPPYTTDEHLIFNSGKMIILDKLLKRLKEKGSRVLIFSQMSRLLDILEDYCYFRDFEYCRIDGSTSHEERIEAIDEYNKPNSEKFVFLLTTRAGGLGINLVTADTVILFDSDWNPQADLQAMDRAHRIGQKKQVHVYRFVTENAIEEKVIERAAQKLRLDQLVIQQGTGKKTASLGNSKDDLLDMIQFGAKNMFEKKASKVTVDADIDDILKKGEQKTQELNAKYQSLGLDDLQKFNGIENQSAYEWNGKSFQKKSNDKVVEWINPSRRERRREQTTYSVDDYYKEIIGGGSKSASKQTPQPKAPRAPKVIHGQDFQFFPKELDALQEKEQLYFKKKVNYKVTSYDITGDIRNEGSDAEEEEGEYKNAANTEGHKGHEELKRRIEEEQEKINSAPDFTQEDELRKQELISKAFTNWNKRDFMAFINACAKYGRDDMENIKKSIDSKTPEEVEVYAKIFWERLKEINGWEKYLHNVELGEKKNEKLKFQETLLRQKIEQCKHPLHELIIQYPPNNARRTYNTLEDKFLLLAVNKYGLRADKLYEKLKQEIMMSDLFTFDWFIKTRTVHELSKRVHTLLTLIVREYEQPDANKKKRSRTSATREDTPLSQNESTRASTVPNLPTTMVTNQKDTNDHVDKRTKIDQEA F71007D7B25C9348 F71007D7B25C9348 itc1_yeast Imitation switch two complex protein 1 G2842 YGL133W ITC1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MVLYKRKPILLPDPKPLPLDLNVQVWHIEETGEWFSSYEEFLERFDFYTRHHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGIRRLDALVEKVYARFKNDFFPGEVVYLRKQKDSSTTSSNSQQSTPQPDDMVEINSVGNPGLPQYQYQRRYVIKEKVQFNATINPESREIVMPAHTKYMLIEEAASSNKSFIVDQGQIYRDRSTFTKHLIKCFFKITLQRASSKMGAPWCVKPEYLAMYGLTMEWPKDMLKYKEDEPVVARRSNSANVSSPESEKNKRQSKSSGKSNTSNDASNKKETKKKRKPTEVNDSENNSSEEDKKKGQNVTSETHSKKRKKEANEEPNTENVESVPTPANAEPQAVTITSIMDDLALPYQHPPNIFPNLTYYNEKLECISLGSTKLSRPFDSFGKLLQAYQFLNTFGSKICLSHFSLDQFITSLKCTDPYELKGEVVLVNIRTQTSKEQEIENNGLPMKNKAETTTEEDSENPSDWQRNSFIRDMIMKRNSDKVEYKIVHDDPASDDILDNINHNGSALLIEVFTALLRLFINEEGDWSCIVVENWIIDDKGVLMERKDERGEGEAKQKRNAHGYFLQDKEKIDNLKDTLKENATEVQKESDAKNETNSESDSKSDSDSEERDPKLEKCLNYRNVNWIERLTKRQFNNSYWLIILLGVLEDCRHLPMYTEFIDSFIEKIIPKDISATQLPKQLWRNFCRKLSFSDKVNALWILVDLVSHFSPDIKAAVDDSMELCGQIRSERFKVARELKTEAAVLSNLQGDLQAIQEKLNKTDENTPSADGADKKDDSESNSEPIDLIIIEKKQKLIEEQDKKVQALQSDKNFLDNCLFENDLQRLKPLGLDRYGNRYFWLDHNGVPFPQYPAGMNETPKSNNSLSYHSGRLLIQGPKASSAKFFLNVSDEQLSNWQKIRNSEGISEATREVFGISKTSSGSYNYVENGIEVELLDSNDRVNPLIELTPIQKKIMDETPSRLLLSPDQWYCIDKLEDLSRIMDWLDNWGRKEHDLLRQIRPIMERIKSSLSLRDHALSLTAFTKNEEKLLKELENNEFTENELNVDSMDVDDKNSGVKSEVDVQVDAEEKREAVIDEKLEVIADELMKLDDSSKTRNVLNRIQELEDQRDELLEQKKSIINSQRPGARILARSERKRTKISRGNKVNKQIEILTDLVNYRHFKAMEDVIAWKNVLANSIWGSSLRKNASGNKRSGVIETVDDKLKDIVGQTSRTVTPAPN 45E4CF8835C7C746 dpoe_yeast DNA polymerase epsilon catalytic subunit A POL2 DUN2 YNL262W N0825 DNA polymerase II subunit A 3'-5' exodeoxyribonuclease protein protein yeast Saccharomyces cerevisiae Baker's yeast MMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGGNSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDCASCDFNRPGKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIATKEDKFKQTSLTKFFSKTKNVPTMGKIKDIEDLFEPTVEEDNAKIKIARTTKKKAVSKRKRNQLTNEEDPLVLPSEIPSMDEDYVGWLNYQKIKWKIQARDRKRRDQLFGNTNSSRERSALGSMIRKQAESYANSTWEVLQYKDSGEPGVLEVFVTINGKVQNITFHIPKTIYMKFKSQTMPLQKIKNCLIEKSSASLPNNPKTSNPAGGQLFKITLPESVFLEEKENCTSIFNDENVLGVFEGTITPHQRAIMDLGASVTFRSKAMGALGKGIQQGFEMKDLSMAENERYLSGFSMDIGYLLHFPTSIGYEFFSLFKSWGDTITILVLKPSNQAQEINASSLGQIYKQMFEKKKGKIETYSYLVDIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQSPFITKLLGTIRLLNQMPIVKLSLNEVLLPQLNWQPTLLKKLVNHVLSSGSWISHLIKLSQYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGGIQNDFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALINDAEGSDLVNNNMGIDDKDAVINSPSEFVHDAFSNDALNVLRGMLKEWWDEALKENSTADLLVNSLASWVQNPNAKLFDGLLRYHVHNLTKKALLQLVNEFSALGSTIVYADRNQILIKTNKYSPENCYAYSQYMMKAVRTNPMFSYLDLNIKRYWDLLIWMDKFNFSGLACIEIEEKENQDYTAVSQWQLKKFLSPIYQPEFEDWMMIILDSMLKTKQSYLKLNSGTQRPTQIVNVKKQDKEDSVENSLNGFSHLFSKPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNPLLELVKSLCHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLSLVVPDFLCEYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKLRSDIESYLIQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNVFKQVAKYYGFDILLSCIADLTI CBCDDE2AB147D65B CBCDDE2AB147D65B dls1_yeast Protein DLS1 YJL065C J1115 HRD167 DPB3-like subunit of ISW2 complex 1 DLS1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNNETSGKETASAPLCSPKLPVEKVQRIAKNDPEYMDTSDDAFVATAFATEFFVQVLTHESLHRQQQQQQQQVPPLPDELTLSYDDISAAIVHSSDGHLQFLNDVIPTTKNLRLLVEENRVRYTTSVMPPNEVYSAYVVNDTAPKPNIVEIDLDNDEDDDEDVTDQE 89B9668F95D64665 dpb4_yeast DNA polymerase epsilon subunit D DPB4 DNA polymerase II subunit D YDR121W protein protein yeast Saccharomyces cerevisiae Baker's yeast MPPKGWRKDAQGNYPTTSYIKEQENITIQDLLFPKSTIVNLAREVPQQSGKKLLINKDASLALQRGATVFVNHLLLFAREIAKSQDKKSCSVDDVLSALDHIGHSALKGPVRDKLDEYQAAVEQRKKEKLDSGEVDADGDIDMGEDKENVPVEKVKEHDEIEEQGDALQDVEESSEKKQKTESQDVETRVQNLEQT 5D061EEA836B8BD3 isw2-dls1-1 1 3 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 7 unspecified role unspecified role prey prey 6 unspecified role unspecified role prey prey association association A large-scale purification of the Isw2 complex by FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column showed Isw2p to copurify with two previously unidentified proteins (Fig. 1A). 1A isw2-dls1-2 1 4 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 3 unspecified role unspecified role prey prey 7 unspecified role unspecified role prey prey association association To further confirm the association of Dpb4p and Yjl065cp with Isw2, we directly purified Yjl065cp via FLAG immunoaffinity chromatography followed by a Source Q anionic-exchange column (Fig. 1B), which yielded a four-subunit Isw2 complex (Itc1p, Isw2p, Dpb4p, and Yjl065cp) and no other proteins at a detectable level. 1B dpb4-isw2-1 2 3 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 5 unspecified role unspecified role prey prey region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 7 unspecified role unspecified role bait bait region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Immunodepletion studies suggested both prey proteins bound to DPB4 Coimmunoprecipitation assay of Dpb4p with both Pol2p and Isw2p. Fig. 2A dsl1-isw2-1 2 4 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 6 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 3 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Immunodepletion of Dls1 resulted in a partial depletion of both Isw2 and Itc1, suggesting the presence of Isw2 and Itc1 populations that do not stably interact with Dls1. we next tested the extent to which Isw2p and Itc1p stably associate with Dls1p by a coimmunoprecipitation experiment Fig. 2C